Genotypic variation in Actinidia deliciosa fruit size and carbohydrate content

In a global and increasingly competitive fresh produce market, more attention is being given to fruit quality traits and consumer satisfaction. Kiwifruit occupies a niche position in the worldwide market, when compared to apples, oranges or bananas. It is a fruit with extraordinarily good nutritional traits, and its benefits to human health have been widely described. Until recently, international trade in kiwifruit was restricted to a single cultivar, but different types of kiwifruit are now becoming available in the market. Effective programmes of kiwifruit improvement start by considering the requirements of consumers, and recent surveys indicate that sweeter fruit with better flavour are generally preferred. There is a strong correlation between at-harvest dry matter and starch content, and soluble solid concentration and flavour when fruit are eating ripe. This suggests that carbon accumulation strongly influences the development of kiwifruit taste. The overall aim of the present study was to determine what factors affect carbon accumulation during Actinidia deliciosa berry development. One way of doing this is by comparing kiwifruit genotypes that differ greatly in their ability to accumulate dry matter in their fruit. Starch is the major component of dry matter content. It was hypothesized that genotypes were different in sink strength. Sink strength, by definition, is the effect of sink size and sink activity. Chapter 1 reviews fruit growth, kiwifruit growth and development and carbon metabolism. Chapter 2 describes the materials and methods used. Chapter 3, 4, 5 and 6 describes different types of experimental work. Chapter 7 contains the final discussions and the conclusions Three Actinidia deliciosa breeding populations were analysed in detail to confirm that observed differences in dry matter content were genetically determined. Fruit of the different genotypes differed in dry matter content mainly because of differences in starch concentrations and dry weight accumulation rates, irrespective of fruit size. More detailed experiments were therefore carried out on genotypes which varied most in fruit starch concentrations to determine why sink strengths were so different. The kiwifruit berry comprises three tissues which differ in dry matter content. It was initially hypothesised that observed differences in starch content could be due to a larger proportion of one or other of these tissues, for example, of the central core which is highest in dry matter content. The study results showed that this was not the case. Sink size, intended as cell number or cell size, was then investigated. The outer pericarp makes up about 60% of berry weight in ‘Hayward’ kiwifruit. The outer pericarp contains two types of parenchyma cells: large cells with low starch concentration, and small cells with high starch concentration. Large cell, small cell and total cell densities in the outer pericarp were shown to be not correlated with either dry matter content or fruit size but further investigation of volume proportion among cell types seemed justified. It was then shown that genotypes with fruit having higher dry matter contents also had a higher proportion of small cells. However, the higher proportion of small cell volume could only explain half of the observed differences in starch content. So, sink activity, intended as sucrose to starch metabolism, was investigated. In transiently starch storing sinks, such as tomato fruit and potato tubers, a pivotal role in carbon metabolism has been attributed to sucrose cleaving enzymes (mainly sucrose synthase and cell wall invertase) and to ADP-glucose pyrophosphorylase (the committed step in starch synthesis). Studies on tomato and potato genotypes differing in starch content or in final fruit soluble solid concentrations have demonstrated a strong link with either sucrose synthase or ADP-glucose pyrophosphorylase, at both enzyme activity and gene expression levels, depending on the case. Little is known about sucrose cleaving enzyme and ADP-glucose pyrophosphorylase isoforms. The HortResearch Actinidia EST database was then screened to identify sequences putatively encoding for sucrose synthase, invertase and ADP-glucose pyrophosphorylase isoforms and specific primers were designed. Sucrose synthase, invertase and ADP-glucose pyrophosphorylase isoform transcript levels were anlayzed throughout fruit development of a selection of four genotypes (two high dry matter and two low dry matter). High dry matter genotypes showed higher amounts of sucrose synthase transcripts (SUS1, SUS2 or both) and higher ADP-glucose pyrophosphorylase (AGPL4, large subunit 4) gene expression, mainly early in fruit development. SUS1- like gene expression has been linked with starch biosynthesis in several crop (tomato, potato and maize). An enhancement of its transcript level early in fruit development of high dry matter genotypes means that more activated glucose (UDP-glucose) is available for starch synthesis. This can be then correlated to the higher starch observed since soon after the onset of net starch accumulation. The higher expression level of AGPL4 observed in high dry matter genotypes suggests an involvement of this subunit in drive carbon flux into starch. Changes in both enzymes (SUSY and AGPse) are then responsible of higher starch concentrations. Low dry matter genotypes showed generally higher vacuolar invertase gene expression (and also enzyme activity), early in fruit development. This alternative cleavage strategy can possibly contribute to energy loss, in that invertases’ products are not adenylated, and further reactions and transport are needed to convert carbon into starch. Although these elements match well with observed differences in starch contents, other factors could be involved in carbon metabolism control. From the microarray experiment, in fact, several kinases and transcription factors have been found to be differentially expressed. Sink strength is known to be modified by application of regulators. In ‘Hayward’ kiwifruit, the synthetic cytokinin CPPU (N-(2-Chloro-4-Pyridyl)-N-Phenylurea) promotes a dramatic increase in fruit size, whereas dry matter content decreases. The behaviour of CPPU-treated ‘Hayward’ kiwifruit was similar to that of fruit from low dry matter genotypes: dry matter and starch concentrations were lower. However, the CPPU effect was strongly source limited, whereas in genotype variation it was not. Moreover, CPPU-treated fruit gene expression (at sucrose cleavage and AGPase levels) was similar to that in high dry matter genotypes. It was therefore concluded that CPPU promotes both sink size and sink activity, but at different “speeds” and this ends in the observed decrease in dry matter content and starch concentration. The lower “speed” in sink activity is probably due to a differential partitioning of activated glucose between starch storage and cell wall synthesis to sustain cell expansion. Starch is the main carbohydrate accumulated in growing Actinidia deliciosa fruit. Results obtained in the present study suggest that sucrose synthase and AGPase enzymes contribute to sucrose to starch conversion, and differences in their gene expression levels, mainly early in fruit development, strongly affect the rate at which starch is therefore accumulated. This results are interesting in that starch and Actinidia deliciosa fruit quality are tightly connected.

Produzione di virus sintetici per lo studio dei meccanismi di interazione coinvolti nell'induzione di resistenza

Beet soil-borne mosaic virus (BSBMV) and Beet necrotic yellow vein virus (BNYVV) are members of Benyvirus genus. BSBMV has been reported only in the United States while BNYVV has a worldwide distribution. Both viruses are vectored by Polymyxa betae, possess similar host ranges, particles number and morphology. Both viruses are not serologically related but have similar genomic organizations. Field isolates consist of four RNA species but some BNYVV isolates contain a fifth RNA. RNAs 1 and 2 are essential for infection and replication while RNAs 3 and 4 play important roles on plant and vector interactions, respectively. Nucleotide and amino acid analyses revealed BSBMV and BNYVV are different enough to be classified in two different species. Additionally in BNYVV/BSBMV mixed infections, a competition was previous described in sugar beet, where BNYVV infection reduces BSBMV accumulation in both susceptible and resistant cultivars. Considering all this observations we hypothesized that BNYVV and BSBMV crossed study, exploiting their similarities and divergences, can improve investigation of molecular interactions between sugar beets and Benyviruses. The main achievement of our research is the production of a cDNA biologically active clones collection of BNYVV and BSBMV RNAs, from which synthetic copies of both Benyviruses can be transcribed. Moreover, through recombination experiments we demonstrated, for the first time, the BNYVV RNA 1 and 2 capability to trans-replicate and encapsidate BSBMV RNA 3 and 4, either the BSBMV RNA 1 and 2 capability to replicate BNYVV RNA2 in planta. We also demonstrated that BSBMV RNA3 support long-distance movement of BNYVV RNA 1 and 2 in B. macrocarpa and that 85 foreign sequence as p29HA, GFP and RFP, are successfully expressed, in C. quinoa, by BSBMV RNA3 based replicon (RepIII) also produced by our research. These results confirm the close correlation among the two viruses. Interestingly, the symptoms induced by BSBMV RNA-3 on C. quinoa leaves are more similar to necrotic local lesions caused by BNYVV RNA-5 p26 than to strongly chlorotic local lesions or yellow spot induced by BNYVV RNA- 3 encoded p25. As previous reported BSBMV p29 share 23% of amino acid sequence identity with BNYVV p25 but identity increase to 43% when compared with sequence of BNYVV RNA-5 p26. Based on our results the essential sequence (Core region) for the longdistance movement of BSBMV and BNYVV in B. macrocarpa, is not only carried by RNA3s species but other regions, perhaps located on the RNA 1 and 2, could play a fundamental role in this matter. Finally a chimeric RNA, composed by the 5’ region of RNA4 and 3’ region of RNA3 of BSBMV, has been produced after 21 serial mechanically inoculation of wild type BSBMV on C. quinoa plants. Chimera seems unable to express any protein, but it is replicated and transcript in planta. It could represent an important tool to study the interactions between Benyvirus and plant host. In conclusion different tools, comprising a method to study synthetic viruses under natural conditions of inoculum through P. Betae, have been produced and new knowledge are been acquired that will allow to perform future investigation of the molecular interactions between sugar beets and Benyviruses.

Identification of surface protein complexes of Streptococcus pyogenes through protein microarray technology

A systematic characterization of the composition and structure of the bacterial cell-surface proteome and its complexes can provide an invaluable tool for its comprehensive understanding. The knowledge of protein complexes composition and structure could offer new, more effective targets for a more specific and consequently effective immune response against a complex instead of a single protein. Large-scale protein-protein interaction screens are the first step towards the identification of complexes and their attribution to specific pathways. Currently, several methods exist for identifying protein interactions and protein microarrays provide the most appealing alternative to existing techniques for a high throughput screening of protein-protein interactions in vitro under reasonably straightforward conditions. In this study approximately 100 proteins of Group A Streptococcus (GAS) predicted to be secreted or surface exposed by genomic and proteomic approaches were purified in a His-tagged form and used to generate protein microarrays on nitrocellulose-coated slides. To identify protein-protein interactions each purified protein was then labeled with biotin, hybridized to the microarray and interactions were detected with Cy3-labelled streptavidin. Only reciprocal interactions, i. e. binding of the same two interactors irrespective of which of the two partners is in solid-phase or in solution, were taken as bona fide protein-protein interactions. Using this approach, we have identified 20 interactors of one of the potent toxins secreted by GAS and known as superantigens. Several of these interactors belong to the molecular chaperone or protein folding catalyst families and presumably are involved in the secretion and folding of the superantigen. In addition, a very interesting interaction was found between the superantigen and the substrate binding subunit of a well characterized ABC transporter. This finding opens a new perspective on the current understanding of how superantigens are modified by the bacterial cell in order to become major players in causing disease.

Genomic characterization of the italian wolf (Canis lupus): the genes involved in black coat colour determination and application of microarray technique for snps detection.

This study provides a comprehensive genetic overview on the endangered Italian wolf population. In particular, it focuses on two research lines. On one hand, we focalised on melanism in wolf in order to isolate a mutation related with black coat colour in canids. With several reported black individuals (an exception at European level), the Italian wolf population constituted a challenging research field posing many unanswered questions. As found in North American wolf, we reported that melanism in the Italian population is caused by a different melanocortin pathway component, the K locus, in which a beta-defensin protein acts as an alternative ligand for the Mc1r. This research project was conducted in collaboration with Prof. Gregory Barsh, Department of Genetics and Paediatrics, Stanford University. On the other hand, we performed analysis on a high number of SNPs thanks to a customized Canine microarray useful to integrate or substitute the STR markers for genotyping individuals and detecting wolf-dog hybrids. Thanks to DNA microchip technology, we obtained an impressive amount of genetic data which provides a solid base for future functional genomic studies. This study was undertaken in collaboration with Prof. Robert K. Wayne, Department of Ecology and Evolutionary Biology, University of California, Los Angeles (UCLA).

Applications of High Speed Configurable Logic Devices in Modern Particle Physics Experiments

Several activities were conducted during my PhD activity. For the NEMO experiment a collaboration between the INFN/University groups of Catania and Bologna led to the development and production of a mixed signal acquisition board for the Nemo Km3 telescope. The research concerned the feasibility study for a different acquisition technique quite far from that adopted in the NEMO Phase 1 telescope. The DAQ board that we realized exploits the LIRA06 front-end chip for the analog acquisition of anodic an dynodic sources of a PMT (Photo-Multiplier Tube). The low-power analog acquisition allows to sample contemporaneously multiple channels of the PMT at different gain factors in order to increase the signal response linearity over a wider dynamic range. Also the auto triggering and self-event-classification features help to improve the acquisition performance and the knowledge on the neutrino event. A fully functional interface towards the first level data concentrator, the Floor Control Module, has been integrated as well on the board, and a specific firmware has been realized to comply with the present communication protocols. This stage of the project foresees the use of an FPGA, a high speed configurable device, to provide the board with a flexible digital logic control core. After the validation of the whole front-end architecture this feature would be probably integrated in a common mixed-signal ASIC (Application Specific Integrated Circuit). The volatile nature of the configuration memory of the FPGA implied the integration of a flash ISP (In System Programming) memory and a smart architecture for a safe remote reconfiguration of it. All the integrated features of the board have been tested. At the Catania laboratory the behavior of the LIRA chip has been investigated in the digital environment of the DAQ board and we succeeded in driving the acquisition with the FPGA. The PMT pulses generated with an arbitrary waveform generator were correctly triggered and acquired by the analog chip, and successively they were digitized by the on board ADC under the supervision of the FPGA. For the communication towards the data concentrator a test bench has been realized in Bologna where, thanks to a lending of the Roma University and INFN, a full readout chain equivalent to that present in the NEMO phase-1 was installed. These tests showed a good behavior of the digital electronic that was able to receive and to execute command imparted by the PC console and to answer back with a reply. The remotely configurable logic behaved well too and demonstrated, at least in principle, the validity of this technique. A new prototype board is now under development at the Catania laboratory as an evolution of the one described above. This board is going to be deployed within the NEMO Phase-2 tower in one of its floors dedicated to new front-end proposals. This board will integrate a new analog acquisition chip called SAS (Smart Auto-triggering Sampler) introducing thus a new analog front-end but inheriting most of the digital logic present in the current DAQ board discussed in this thesis. For what concern the activity on high-resolution vertex detectors, I worked within the SLIM5 collaboration for the characterization of a MAPS (Monolithic Active Pixel Sensor) device called APSEL-4D. The mentioned chip is a matrix of 4096 active pixel sensors with deep N-well implantations meant for charge collection and to shield the analog electronics from digital noise. The chip integrates the full-custom sensors matrix and the sparsifification/readout logic realized with standard-cells in STM CMOS technology 130 nm. For the chip characterization a test-beam has been set up on the 12 GeV PS (Proton Synchrotron) line facility at CERN of Geneva (CH). The collaboration prepared a silicon strip telescope and a DAQ system (hardware and software) for data acquisition and control of the telescope that allowed to store about 90 million events in 7 equivalent days of live-time of the beam. My activities concerned basically the realization of a firmware interface towards and from the MAPS chip in order to integrate it on the general DAQ system. Thereafter I worked on the DAQ software to implement on it a proper Slow Control interface of the APSEL4D. Several APSEL4D chips with different thinning have been tested during the test beam. Those with 100 and 300 um presented an overall efficiency of about 90% imparting a threshold of 450 electrons. The test-beam allowed to estimate also the resolution of the pixel sensor providing good results consistent with the pitch/sqrt(12) formula. The MAPS intrinsic resolution has been extracted from the width of the residual plot taking into account the multiple scattering effect.

LrhA als Regulator der Flagellen, Motilität, Chemotaxis und Typ 1 Fimbrien in Escherichia coli

Das lrhA-Gen von E. coli kodiert für einen Transkriptionsregulator der LysR-Familie. Die Funktion von LrhA war ungeklärt und sollte durch Vergleich der Gesamt-mRNA aus einem E. coli-Wildtyp und einer isogenen lrhA-Mutante mit Hilfe von Genomanalysen untersucht werden. In der lrhA-Mutante war der mRNA-Gehalt vieler Gene um den Faktor 3 bis 80 erhöht. Es handelt sich um Flagellen-, Motilitäts- und Chemotaxisgene, bzw. um Gene der Typ 1 Fimbrien. Diese Ergebnisse wurden in Expressionsmessungen bestätigt. LrhA war in der Lage an den Promotor von flhDC zu binden, aber nicht an die Promotoren der übrigen Gene für Motilität und Chemotaxis. FlhDC kodiert für den übergeordneten Regulator FlhD2C2 der Fagellensynthese.LrhA war außerdem in der Lage an die Promotoren der Gene für Typ 1 Fimbrien fimA und fimE zu binden. Typ 1 Fimbrien stellen in E. coli Virulenzfaktoren dar. Eine Regulation weiterer Virulenzfaktoren durch LrhA konnte in DNA-Pathoarrays ausgeschlossen werden.LrhA ist damit ein wichtiger Transkriptionsregulator, der die Expression der Gene für Flagellen, Motilität, Chemotaxis und Typ 1 Fimbrien reguliert. FlhDC, fimA und fimE stellen dabei direkte Zielgene von LrhA dar. Außerdem konnte eine positive Autoregulation von LrhA nachgewiesen werden.

Aufbau des GDH-Experiments und Messung der Helizitätsabhängigkeit von gamma p p pi + pi- von der Schwelle bis 800 MeV

Das Experiment zur Überprüfung der Gerasimov-Drell-Hearn(GDH)-Summenregel am Mainzer Mikrotron diente zur Messunghelizitätsabhängiger Eigenschaften der Photoproduktion amProton. Hierbei konnten neben den totalen Photoabsorptionswirkungsquerschnitten auch Querschnitte partieller Kanäle der Einpion-, Zweipion- und Eta-Produktion bestimmt werden. Für die möglichen Doppel-Pion-Reaktionen sind zur Zeit nur wenig Information vorhanden. Daher sind die Reaktionsmechanismen der Doppel-Pion-Photoproduktion weitgehend noch unverstanden. Aus diesem Grund ist die Untersuchung weiterer Observablenerforderlich. Die Helizitätsabhängigkeit stellt eine solcheneue Observable dar und kann dadurch gemessen werden, daßein zirkular polarisiertes Photon mit einem longitudinalpolarisierten Nukleon wechselwirkt. Der Photonspin beträgt1 und der Fermionenspin des Nukleons beträgt 1/2.Die Spins koppeln zu 3/2 und 1/2. Dies liefert diehelizitätsabhängigen Wirkungsquerschnitte.Diese Dissertation beschreibt den Aufbau des Mainzer GDH-Experiments und die technische Realisation der Messung helizitätsabhängiger Photoabsorptionswirkungsquerschnitte. Die Helizitätsabhängigkeit der doppelt geladenen Doppel-Pion-Photoproduktion am Proton wurde anhand der gemessenen Daten untersucht. Diese Reaktion ist ein Zweistufenprozeß, wobei das angeregte Nukleon resonant oder nicht-resonant in die Endzustandsteilchen zerfällt. Durch die helizitätsabhängigen Daten wurden Freiheitsgradein der Doppel-Pion-Photoproduktion eingeschränkt, wodurch eine Verbesserung der Modelle der Gent-Mainz- und der Valencia-Gruppe ermöglicht wurde. Die im Rahmen dieser Arbeit ermittelten Daten haben zusätzlich eine Motivation für weitere Interpretationsansätze durch die genanntenTheoriegruppen geschaffen.

An evolutionary approach to the design of experiments for combinatorial optimization with an application to enzyme engineering

In a large number of problems the high dimensionality of the search space, the vast number of variables and the economical constrains limit the ability of classical techniques to reach the optimum of a function, known or unknown. In this thesis we investigate the possibility to combine approaches from advanced statistics and optimization algorithms in such a way to better explore the combinatorial search space and to increase the performance of the approaches. To this purpose we propose two methods: (i) Model Based Ant Colony Design and (ii) Naïve Bayes Ant Colony Optimization. We test the performance of the two proposed solutions on a simulation study and we apply the novel techniques on an appplication in the field of Enzyme Engineering and Design.

Sleep-related changes in blood pressure in hypocretin-deficient narcoleptic mice

Objectives. Blood pressure (BP) physiologically has higher and lower values during the active and rest period, respectively. Subjects failing to show the appropriate BP decrease (10-20%) on passing form diurnal activity to nocturnal rest and sleep have increased risk of target organ damage at the cardiac, vascular and cerebrovascular levels. Hypocretin (HCRT) releasing neurons, mainly located in the lateral hypothalamus, project widely to the central nervous system. Thus HCRT neurons are involved in several autonomic functions, including BP regulation. HCRT neurons also play a key role in wake-sleep cycle regulation, the lack of which becomes evident in HCRT-deficient narcoleptic patients. I investigated whether chronic lack of HCRT signaling alters BP during sleep in mouse models of narcolepsy. Methods. The main study was performed on HCRT-ataxin3 transgenic mice (TG) with selective post-natal ablation of HCRT neurons, HCRT gene knockout mice (KO) with preserved HCRT neurons, and Wild-Type control mice (WT) with identical genetic background. Experiments where replicated on TG and WT mice with hybrid genetic background (hTG and hWT, respectively). Mice were implanted with a telemetric pressure transducer (TA11PA-C10, DSI) and electrodes for discriminating wakefulness (W), rapid-eye-movement sleep (REMS) and non-REMS (NREMS). Signals were recorded for 3 days. Mean BP values were computed in each wake-sleep state and analyzed by ANOVA and t-test with significance at p<0.05. Results. The decrease in BP between either NREMS or REMS and W was significantly blunted in TG and KO with respect to WT as well as in hTG with respect to hWT. Conclusions. Independently from the genetic background, chronic HCRT deficiency leads to a decreased BP difference between W and sleep potentially adverse in narcoleptic subjects. These data suggest that HCRT play an important role in the sleep-dependent cardiovascular control.

Genomische Struktur und Promotorcharakterisierung des humanen ADAM10-Gens

Das ADAM10-Gen kodiert für eine membrangebundene Disintegrin-Metalloproteinase, die das Amyloidvorläuferprotein spaltet. Im Mausmodell konnte bewiesen werden, dass die Überexpression von ADAM10 die Plaquebildung vermindern und das Langzeitgedächtnis verbessert. Aus diesem Grund ist es für einen möglichen Therapieansatz für die Alzheimer’sche Erkrankung erforderlich, die Organisation des humanen ADAM10-Gens und seines Promotors aufzuklären. Beim Vergleich der genomischen Sequenzen von humanem und murinem ADAM10 zeigte sich eine hohe Übereinstimmung. Beide Gene umfassen 160 kbp und bestehen aus 16 Exons. Die ersten 500 bp stromaufwärts vom Translationsstartpunkt zwischen dem Menschen, der Maus und der Ratte sind hoch konserviert. Diese Region beinhaltet spezifische regulatorische Elemente, die die ADAM10-Transkription modulieren. In den ersten 2179 bp stromaufwärts vom humanen ADAM10-Translationsstartpunkt fanden sich einige potentiellen Transkriptionsfaktor-bindungsstellen (Brn-2, SREBP, Oct-1, Creb1/cJun, USF, Maz, MZF-1, NFkB und CDPCR3HD). Es wurde eine charakteristische GC-Box und eine CAAT-Box, aber keine TATA-Box identifiziert. Nach Klonierung dieser 2179 bp großen Region wurde eine starke Promotoraktivität, insbesondere in neuronalen Zelllinien, gefunden. Bei der Analyse von Deletionskonstrukten wurde die Region zwischen -508 und -300 als essentiell für die Transkriptionsaktivierung bestimmt. Die Promotoraktivität wird zudem streng herunterreguliert, wenn in die Region 317 bp stromaufwärts vom Startpunkt der Translation eine Punktmutation eingeführt wird. Diese per Computeranalyse als USF-Bindungsstelle deklarierte Region spielt eine zentrale Rolle bei der ADAM10-Transkription. Im EMSA wurde eine Protein-DNA-Interaktion für diese Region gezeigt. Durch transienten Transfektionen in Schneider Drosophila Insektenzellen konnte nachgewiesen werden, dass die Überexpression von Sp1 und USp3 für die ADAM10-Promotoraktivität entscheidend ist. In EMSA-Studien bestätigte sich eine Protein-DNA-Interaktion für die Region -366 bp stromaufwärts vom Translationsstartpunkt. Die Punktmutation in der CAAT-Box veränderte die die Promotoraktivität nicht. Da weiterhin für diese potentielle Bindungsstelle kein Bindungsfaktor vorausgesagt wurde, scheint die CAAT-Box keine Bedeutung bei der Promotorregulation zu spielen. Schließlich fand sich im EMSA eine Protein-DNA-Interaktion für die Bindungsstelle 203 bp stromaufwärts vom Translationsstartpunkt. Diese in Computeranalysen als RXR-Bindungsstelle identifizierte Region ist ebenfalls von Bedeutung in der Promotorregulation. Auf der Suche nach Substanzen, die die ADAM10-Promotoraktivität beeinflussen, wurde ein negativer Effekt durch die apoptoseauslösende Substanz Camptothecin und ein positiver Effekt durch die zelldifferenzierungsauslösende Substanz all-trans Retinsäure festgestellt. Mit dieser Arbeit wurde die genomische Organisation des ADAM10-Gens zusammen mit dem zugehörigen Promotor aufgeklärt und ein neuer Regulationsmechanismus für die Hochregulation der Expression der alpha-Sekretase ADAM10 gefunden. Im Weiteren sollen nun die genauen Mechanismen bei der Hochregulation der alpha-Sekretase ADAM10 durch Retinsäure untersucht und durch Mikroarray-Analysen an RNA-Proben transgener Mäuse, welche ADAM10 überexpremieren, neue therapeutische Ansätze zur Behandlung der Alzheimer´schen Erkrankung identifiziert werden.

Bioinformatic methods in applied genomic research

Here I will focus on three main topics that best address and include the projects I have been working in during my three year PhD period that I have spent in different research laboratories addressing both computationally and practically important problems all related to modern molecular genomics. The first topic is the use of livestock species (pigs) as a model of obesity, a complex human dysfunction. My efforts here concern the detection and annotation of Single Nucleotide Polymorphisms. I developed a pipeline for mining human and porcine sequences. Starting from a set of human genes related with obesity the platform returns a list of annotated porcine SNPs extracted from a new set of potential obesity-genes. 565 of these SNPs were analyzed on an Illumina chip to test the involvement in obesity on a population composed by more than 500 pigs. Results will be discussed. All the computational analysis and experiments were done in collaboration with the Biocomputing group and Dr.Luca Fontanesi, respectively, under the direction of prof. Rita Casadio at the Bologna University, Italy. The second topic concerns developing a methodology, based on Factor Analysis, to simultaneously mine information from different levels of biological organization. With specific test cases we develop models of the complexity of the mRNA-miRNA molecular interaction in brain tumors measured indirectly by microarray and quantitative PCR. This work was done under the supervision of Prof. Christine Nardini, at the “CAS-MPG Partner Institute for Computational Biology” of Shangai, China (co-founded by the Max Planck Society and the Chinese Academy of Sciences jointly) The third topic concerns the development of a new method to overcome the variety of PCR technologies routinely adopted to characterize unknown flanking DNA regions of a viral integration locus of the human genome after clinical gene therapy. This new method is entirely based on next generation sequencing and it reduces the time required to detect insertion sites, decreasing the complexity of the procedure. This work was done in collaboration with the group of Dr. Manfred Schmidt at the Nationales Centrum für Tumorerkrankungen (Heidelberg, Germany) supervised by Dr. Annette Deichmann and Dr. Ali Nowrouzi. Furthermore I add as an Appendix the description of a R package for gene network reconstruction that I helped to develop for scientific usage (http://www.bioconductor.org/help/bioc-views/release/bioc/html/BUS.html).